Variant report

Variant	rs961203
Chromosome Location	chr10:6481404-6481405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:6472528..6475094-chr10:6479400..6481457,2	K562	blood:
2	chr10:6478418..6480060-chr10:6480700..6482400,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10508308	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10752329	0.96[ASN][1000 genomes]
rs10752330	0.96[ASN][1000 genomes]
rs10906504	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11258500	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11258501	0.85[CEU][hapmap]
rs11258515	0.86[ASN][1000 genomes]
rs11258589	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11258612	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11258967	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11596750	0.89[JPT][hapmap]
rs12572911	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs12770464	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12775595	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12780187	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17155850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17155855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236380	0.89[JPT][hapmap]
rs2296125	0.85[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs34316142	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35935618	0.86[ASN][1000 genomes]
rs3793722	0.88[JPT][hapmap]
rs3793724	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3793725	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3793726	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3793730	1.00[YRI][hapmap]
rs4237436	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4750422	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs590467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs631968	0.89[JPT][hapmap]
rs6602745	1.00[YRI][hapmap]
rs681071	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs686333	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs688853	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes]
rs71479777	0.86[ASN][1000 genomes]
rs7893745	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7898408	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7910745	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7911478	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7918923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9633784	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs961203	SCN3B	trans	brain	seeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6456200-6496600	Weak transcription	Pancreas	Pancrea
2	chr10:6464200-6487200	Strong transcription	Fetal Thymus	thymus
3	chr10:6464400-6485800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:6464600-6490600	Strong transcription	Primary T cells from cord blood	blood
5	chr10:6464800-6487400	Strong transcription	Thymus	Thymus
6	chr10:6465800-6486600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr10:6465800-6496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:6465800-6496600	Weak transcription	Psoas Muscle	Psoas
9	chr10:6465800-6501400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:6466000-6486600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:6466400-6487800	Weak transcription	Fetal Stomach	stomach
12	chr10:6467000-6487200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr10:6467400-6496200	Weak transcription	Lung	lung
14	chr10:6467600-6487600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr10:6467800-6486000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:6467800-6487000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:6467800-6487400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:6467800-6487600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr10:6468000-6483800	Weak transcription	K562	blood
20	chr10:6468000-6487600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr10:6468000-6487800	Weak transcription	Brain Angular Gyrus	brain
22	chr10:6468200-6496800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr10:6468400-6484600	Weak transcription	Spleen	Spleen
24	chr10:6469800-6484000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:6470200-6483400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr10:6471200-6490200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:6473600-6483600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr10:6473600-6487800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:6474200-6490400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:6474400-6487400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr10:6476800-6484600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:6477200-6482000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr10:6477400-6487800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr10:6477400-6503600	Weak transcription	Gastric	stomach
35	chr10:6478600-6484600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:6478600-6485600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:6478800-6491000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr10:6479200-6487400	Weak transcription	Brain Anterior Caudate	brain
39	chr10:6479400-6482400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:6479400-6483400	Weak transcription	Aorta	Aorta
41	chr10:6479800-6487800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:6480200-6486800	Strong transcription	Dnd41	blood
43	chr10:6480200-6501000	Weak transcription	Ovary	ovary
44	chr10:6480400-6484200	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr10:6480400-6484400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr10:6480400-6484800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:6480600-6482600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr10:6480600-6484000	Strong transcription	Fetal Muscle Leg	muscle
49	chr10:6480600-6484600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr10:6480800-6482400	Strong transcription	Brain Hippocampus Middle	brain

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